At a glance

This report contains visualisations of statistics that can help in understanding the results from the wf-human-variation workflow. Each section contains different plots or tables, and in general the results are broken down by sample. You can quickly jump to an individual section with the links in the header bar. Please note, as a BED file has been provided, the statistics will correspond to the regions defined in that file.

Sample total reads

27943

Sample read N50

10672 bp

Sample mean coverage

36.266x

Summary

Metric Value Percentage
Reads 27,943
100.0%
Unmapped reads 0
0.0%
Bases 215,730,931
100.0%

Read statistics

This section displays the read statistics for the sample processed. A description of each plot is as follows:

Read quality: read quality (range cropped to 4-30) vs. the number of reads.
Read length: read length vs. the number of reads.
Base yield above read length: base yield above a given read length.
Accuracy: mapping accuracy (ranging from 0-100%) vs. the number of reads.
Coverage: coverage (proportion of read spanned by alignment) vs. the number of reads.

Depth of coverage

This section illustrates the depth of coverage of the reference genomes. The plot shows coverage vs. genomic position (note that the coordinates on the x-axis are the positions along the concatenated reference including all reference sequences in the respective reference file).

Software versions

Name Version
mosdepth 0.3.3
minimap2 2.24-r1122

Workflow parameters

Key Value
out_dir .
bam /external/data/lucy/20241107-BiomarkerProject/merged_bams
ref /external/analyses/lucy/nanopore_multiBM_pipeline/resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
bed /external/analyses/lucy/nanopore_multiBM_pipeline/results/panel.bed
sample_name test6
sv True
snp True
mod True
str True
phased True
override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac@v4.1.0
output_gene_summary True
output_xam_fmt bam
modkit_args --preset traditional
bam_min_coverage 0
threads 24
ubam_map_threads 24
ubam_sort_threads 24
cnv False
sv_benchmark False
sv_benchmark_vcf None
sv_benchmark_bed None
downsample_coverage False
downsample_coverage_target 60
downsample_coverage_margin 1.1
depth_window_size 25000
haplocheck False
mitogenome None
igv False
ubam_bam2fq_threads 1
annotation True
clair3_model_path None
use_longphase False
ctg_name None
include_all_ctgs False
ref_pct_full 0.1
var_pct_full 0.7
GVCF False
base_err 0.001
gq_bin_size 5
snp_min_af 0.08
indel_min_af 0.15
vcf_fn None
min_contig_size 0
min_mq 5
min_cov 2
min_qual 2
refine_snp_with_sv True
tr_bed None
min_sv_length 30
min_read_support auto
min_read_support_limit 2
cluster_merge_pos 150
sniffles_args None
use_qdnaseq False
qdnaseq_bin_size 500
spectre_args None
force_strand False
modkit_threads 4
sex None
depth_intervals False
output_report True
partner None